GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Shewanella amazonensis SB2B

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  147 bits (371), Expect = 3e-40
 Identities = 88/255 (34%), Positives = 140/255 (54%), Gaps = 16/255 (6%)

Query: 7   STQNASQALLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEE 66
           +T+   + LL+I  + K +  +  +  V LT+ +G +  L+G SGSGK+TLLR +   E 
Sbjct: 12  TTKTQDEVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFER 71

Query: 67  FQGGQILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGL 126
              G+I LDG+ I                +  +     M FQ + LFPH+T  QN+  G 
Sbjct: 72  PTEGRIYLDGQDI--------------TDLPPYERPINMMFQSYALFPHMTVEQNIAFG- 116

Query: 127 LKVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDE 186
           LK  K+ K +     ++ L+ V + +     P QLSGGQ+QRVA+AR++A  P L+L DE
Sbjct: 117 LKQDKMSKADISQRVQEMLKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDE 176

Query: 187 VTSALDPELVGEV-LSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPK 245
              ALD +L  ++ L V++ L   G+T ++VTH+   A  ++ +I  M+ G I + G P 
Sbjct: 177 PMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPM 236

Query: 246 ELFERPQSPRLAEFL 260
           +++E P S  +AEF+
Sbjct: 237 DIYESPNSRMIAEFI 251


Lambda     K      H
   0.319    0.135    0.379 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 216
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 265
Length of database: 378
Length adjustment: 27
Effective length of query: 238
Effective length of database: 351
Effective search space:    83538
Effective search space used:    83538
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory